MathFeature: feature extraction package for DNA, RNA and protein sequences based on mathematical descriptors

Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring

(2021) Ryan B. Ghannam et al.   Computational and Structural Biotechnology Journal

Feature extraction approaches for biological sequences: a comparative study of mathematical features

(2021) Robson P Bonidia et al.   BRIEFINGS IN BIOINFORMATICS

iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization

(2021) Zhen Chen et al.   NUCLEIC ACIDS RESEARCH

SubFeat: Feature Subspacing Ensemble Classifier for Function Prediction of DNA, RNA and Protein Sequences

(2021) H.M.Fazlul Haque et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

PVPred-SCM: Improved Prediction and Analysis of Phage Virion Proteins Using a Scoring Card Method

(2020) Phasit Charoenkwan et al.   Cells

Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study

(2020) Gurjit S. Randhawa et al.   PLoS One

Meta-iPVP: a sequence-based meta-predictor for improving the prediction of phage virion proteins using effective feature representation

(2020) Phasit Charoenkwan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Prediction of Anticancer Peptides Using a Low-Dimensional Feature Model

(2020) Qingwen Li et al.   Frontiers in Bioengineering and Biotechnology

A diagnostic genomic signal processing (GSP)-based system for automatic feature analysis and detection of COVID-19

(2020) Safaa M Naeem et al.   BRIEFINGS IN BIOINFORMATICS

Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations

(2020) Murilo Henrique Anzolini Cassiano et al.   mSystems

Recent Advances of Deep Learning in Bioinformatics and Computational Biology

(2019) Binhua Tang et al.   Frontiers in Genetics

PyFeat: A Python-based Effective Feature Generation Tool for DNA, RNA, and Protein Sequences

(2019) Rafsanjani Muhammod et al.   BIOINFORMATICS

Seq2Feature: a comprehensive web-based feature extraction tool

(2019) Rahul Nikam et al.   BIOINFORMATICS

Physicochemical n‐Grams Tool: A tool for protein physicochemical descriptor generation via Chou’s 5‐step rule

(2019) Shubham Vishnoi et al.   Chemical Biology & Drug Design

BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches

(2019) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences

(2018) Zhen Chen et al.   BIOINFORMATICS

BASiNET—BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification

(2018) Eric Augusto Ito et al.   NUCLEIC ACIDS RESEARCH

PVP-SVM: Sequence-Based Prediction of Phage Virion Proteins Using a Support Vector Machine

(2018) Balachandran Manavalan et al.   Frontiers in Microbiology

Machine learning meets genome assembly

(2018) Kleber Padovani de Souza et al.   BRIEFINGS IN BIOINFORMATICS

Identifying sigma70 promoters with novel pseudo nucleotide composition

(2017) Hao Lin et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

(2017) Yu-Jian Kang et al.   NUCLEIC ACIDS RESEARCH

On DNA numerical representations for genomic similarity computation

(2017) Gerardo Mendizabal-Ruiz et al.   PLoS One

Numerical encoding of DNA sequences by chaos game representation with application in similarity comparison

(2016) Tung Hoang et al.   GENOMICS

Virus Variation Resource – improved response to emergent viral outbreaks

(2016) Eneida L. Hatcher et al.   NUCLEIC ACIDS RESEARCH

iACP: a sequence-based tool for identifying anticancer peptides

(2016) Wei Chen et al.   Oncotarget

ProFET: Feature engineering captures high-level protein functions

(2015) Dan Ofer et al.   BIOINFORMATICS

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

(2015) Tsu-Pei Chiu et al.   BIOINFORMATICS

protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences

(2015) Nan Xiao et al.   BIOINFORMATICS

repRNA: a web server for generating various feature vectors of RNA sequences

(2015) Bin Liu et al.   MOLECULAR GENETICS AND GENOMICS

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

(2015) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects

(2014) Bin Liu et al.   BIOINFORMATICS

PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions

(2014) Wei Chen et al.   BIOINFORMATICS

SPiCE: a web-based tool for sequence-based protein classification and exploration

(2014) Bastiaan A van den Berg et al.   BMC BIOINFORMATICS

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

(2014) Aimin Li et al.   BMC BIOINFORMATICS

A measure of DNA sequence similarity by Fourier Transform with applications on hierarchical clustering

(2014) Changchuan Yin et al.   JOURNAL OF THEORETICAL BIOLOGY

Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis

(2014) Hui Ding et al.   Molecular BioSystems

propy: a tool to generate various modes of Chou’s PseAAC

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

Applying Shannon's information theory to bacterial and phage genomes and metagenomes

(2013) Sajia Akhter et al.   Scientific Reports

Shannon, Rényie and Tsallis entropy analysis of DNA using phase plane

(2011) J.A. Tenreiro Machado et al.   NONLINEAR ANALYSIS-REAL WORLD APPLICATIONS

Using graph theory to analyze biological networks

(2011) Georgios A Pavlopoulos et al.   BioData Mining

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

PseAAC: A flexible web server for generating various kinds of protein pseudo amino acid composition

(2007) Hong-Bin Shen et al.   ANALYTICAL BIOCHEMISTRY